Reading
CIFTI files organize the gray matter of the brain into “greyordinates”: vertices representing the left and right cortical surfaces, and voxels representing the subcortical gray matter structures and the cerebellum. A CIFTI file consists of two parts: (1) a NIFTI XML header which contains all the metadata including medial wall locations, subcortical structure labels, and the subcortical volumetric mask; and (2) a matrix representing all the greyordinate data. These components are read in together with read_cifti:
basename(cifti_fnames["dscalar"])
## [1] "Conte69.MyelinAndCorrThickness.6k_fs_LR.dscalar.nii"
xii <- read_xifti(cifti_fnames["dscalar"])
xii
## Brain Structures: left cortex, right cortex
## left cortex: 5412 surface vertices, 2 measurements.
## right cortex: 5434 surface vertices, 2 measurements.
## Intent: 3006 (dscalar).
#plot(xii) # for visualization, we'll get to that next!
By default, read_cifti only reads in the left and right cortex data. The subcortical data can be included by using the argument brainstructures="all". Other brainstructure combinations can be specified too, e.g. brainstructures=c("left", "subcortical"). The full set of choices for brainstructures is any combination of "left", "right" and "subcortical", or "all" for all three.
The resulting object produced by read_cifti is a "xifti" with components data (the greyordinate data matrix, separated by brainstructure), meta (metadata, most of which is from the NIFTI XML header), and surf (surface geometry). The last component distinguishes a "xifti" from a CIFTI: the left and right cortical surface geometries are not included in CIFTI files, so they must be read from separate surface GIFTI files (ending in surf.gii). The surface must be compatible: the number of vertices must be the same, and each vertex in the CIFTI data must correspond to the vertex location in the corresponding GIFTI surface file. In this way, a "xifti" represents a combination of a CIFTI file with compatible GIFTI files for the cortical mesh.
We can add GIFTI surface geometries like so:
basename(cifti_fnames["dtseries"])
## [1] "Conte69.MyelinAndCorrThickness.32k_fs_LR.dtseries.nii"
xii <- read_xifti(cifti_fnames["dtseries"])
xii <- add_surf(xii, surfL=surfL_fname, surfR=surfR_fname)
xii
## Brain Structures: left cortex, right cortex
## left cortex: 30424 surface vertices, 2 measurements.
## left surface model is present.
## right cortex: 30527 surface vertices, 2 measurements.
## right surface model is present.
## Intent: 3002 (dtseries).
Alternatively, we could have provided the surface geometries at the outset of reading the CIFTI file:
xii2 <- read_xifti(cifti_fnames["dtseries"], surfL_fname=surfL_fname, surfR_fname=surfR_fname)
all.equal(xii, xii2) # same result
## [1] TRUE
To only read the CIFTI header, use info_cifti:
xii_info <- ciftiTools::info_cifti(cifti_fnames["dscalar"])
str(xii_info) # shows header structure
## List of 3
## $ cortex :List of 2
## ..$ medial_wall_mask:List of 2
## .. ..$ left : logi [1:5762] TRUE TRUE TRUE TRUE TRUE TRUE ...
## .. ..$ right: logi [1:5762] TRUE TRUE TRUE TRUE TRUE TRUE ...
## ..$ resamp_res : NULL
## $ subcort:List of 3
## ..$ labels : NULL
## ..$ mask : NULL
## ..$ trans_mat: NULL
## $ cifti :List of 4
## ..$ intent : num 3006
## ..$ brainstructures: chr [1:2] "left" "right"
## ..$ names : chr [1:2] "MyelinMap_BC_decurv" "corrThickness"
## ..$ misc :List of 4
## .. ..$ ParentProvenance : chr "C:\\Users\\damon\\AppData\\Local\\Temp\\Rtmp2X6THF/resampled_6000_Conte69.MyelinAndCorrThickness.32k_fs_LR.L.fu"| __truncated__
## .. ..$ ProgramProvenance: chr "Connectome Workbench\nType: Command Line Application\nVersion: 1.4.2\nQt Compiled Version: 5.7.0\nQt Runtime Ve"| __truncated__
## .. ..$ Provenance : chr "C:\\Users\\damon\\Desktop\\WORKBE~1\\BIN_WI~1\\WB_COM~1.EXE -cifti-create-dense-scalar C:\\Users\\damon\\Deskto"| __truncated__
## .. ..$ WorkingDirectory : chr "C:/Users/damon/Desktop/ciftiTools/vignettes"
To only read in certain columns, use the idx argument:
read_xifti(cifti_fnames["dtseries"], idx=2) # second column only
## Brain Structures: left cortex, right cortex
## left cortex: 30424 surface vertices, 1 measurements.
## right cortex: 30527 surface vertices, 1 measurements.
## Intent: 3002 (dtseries).
Writing
When "xifti" object is written to files, the CIFTI components are placed in a CIFTI file and the surface geometries, if any, are placed in GIFTI files.
out_dir <- "output"
write_xifti(
xii, file.path(out_dir, "my_cifti.dtseries.nii"),
file.path(out_dir, "my_L.surf.gii"), file.path(out_dir, "my_R.surf.gii")
)
## Writing left cortex.
## Writing right cortex.
## Creating CIFTI file from separated components.
## Writing surface geometry GIFTI(s).
With separate_cifti, a CIFTI can be separated and written into its component parts: the cortical data can be written to GIFTI metric files, and the subcortical data can be written to a NIFTI file. In addition, any ROIs or labels will also be written to files. The files are automatically named unless a new file name is provided.
# Use default names for everything except left cortex
separated_fnames = separate_cifti(
cifti_fnames["dscalar_ones"], brainstructures="all",
cortexL_fname="my_left_cortex.func.gii", write_dir = out_dir
)
# Files written to `out_dir`, or current working dir. if not specified
basename(separated_fnames)
## [1] "my_left_cortex.func.gii" "ones_1k.ROI_L.func.gii"
## [3] "ones_1k.R.func.gii" "ones_1k.ROI_R.func.gii"
## [5] "ones_1k.nii" "ones_1k.labels.nii"
## [7] "ones_1k.ROI.nii"
Separated files can be read into R with the oro.nifti/RNifti and gifti packages, and combined into a "xifti" object with as.xifti.
